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Marco Cavaleri,1 Stefano Tigano,1,2 Roberta Nicoletti,1,2 Valeria La Rosa,1,2 Alberto Terminella,3 Giacomo Cusumano,3 Filippo Sanfilippo,1 Marinella Astuto1,2 1Department of General Surgery and Medical-Surgical Specialties, Section of Anaesthesia and Intensive Care, University Hospital “G. Rodolico”, University of Catania, Catania, 95123, Italy; 2School of Anaesthesia and Intensive Care, University Hospital “G. Rodolico”, University of Catania, Catania, 95123, Italy; 3Thoracic Surgery Unit, Department of General Surgery and Medical-Surgical Specialties, University Hospital “G. Rodolico” - San Marco Hospital, Catania, 95121, ItalyCorrespondence: Marco CavaleriDepartment of General Surgery and Medical-Surgical Specialties, Section of Anaesthesia and Intensive Care, University Hospital “G. Rodolico”, University of Catania, Via Santa Sofia 78, Catania, 95123, ItalyTel +393339369927Email markuscava@gmail.comIntroduction: The erector spinae plane block (ESPB) is a recently implemented analgesic technique initially reported for thoracic analgesia and subsequently adopted for both intra- and postoperative pain management. Thoracic surgery is among the most painful surgical procedures, even when conducted with minimally invasive approach. Robotic-assisted thoracic surgery (RATS) challenges the traditional analgesic regimens as one of its aims is to decrease the patient’s length of stay (LOS) whilst achieving optimal postoperative pain management. Furthermore, there is lots of growing evidence on the impact of poorly controlled postoperative pain (PP) on the development of chronic post-surgical pain (CPSP). In these case series, we aim to describe our preliminary experience of postoperative pain management with continuous ESPB in the field of RATS.Case Series Presentation: In eight consecutive patients undergoing elective RATS procedure, we performed the ESPB after surgery with an initial bolus of local anesthetic followed by catheter insertion for continuous infusion. The infusion of local anesthetic lasted for the first two postoperative days. The effectiveness of the ESPB was evaluated through serial pain assessment with numeric rate scale (NRS) score, both at rest and during movement every 6 hours. Any analgesic rescue drug prescription was reported. We noted that the ESPB strongly reduced the prescription of opioids and of rescue analgesic. In our series, only one patient needed opioids during the first two postoperative days, and no rescue analgesic administration was noted in the remaining cases.Conclusion: We report a small but promising experience regarding postoperative pain management with continuous ESPB performed after RATS. We implemented the ESPB before surgery. Larger studies on postoperative pain management with continuous regional blocks in thoracic surgery are warranted.Keywords: pain management, regional block, thoracic surgery, postoperative care

Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.

Warming climate and increasing desertification urge the identification of genes involved in heat and dehydration tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate a chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for a signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another congeneric desert specialist (Peromyscus eremicus) and a widely distributed habitat generalist (Peromyscus maniculatus), that may be locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of parallel evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in the P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic tuning (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important for accommodating hot and dry environmental conditions.

Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive under scenarios of local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and often associated with tightly-linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of discrete genomic regions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (Menidia menidia) from two locally adapted populations and their F1 hybrids, reared under two different temperatures. We found substantial divergence in gene expression and thermal plasticity, with up to 31% of genes being differentially expressed, and primarily trans-rather than cis-regulatory divergence between populations, despite ongoing gene flow. Substantially reduced thermal plasticity, temperature-dependent gene misexpression and the disruption of co-expression networks in hybrids point toward a role of regulatory incompatibilities in maintaining local adaptation, particularly under colder temperatures, which appear more challenging for this species. Adaptive chromosomal inversions seem to play an important role in gene regulatory divergence through the accumulation of regulatory incompatibilities but are not consistently enriched for divergently regulated genes. Together, these results highlight that gene regulation can diverge substantially among populations connected by strong gene flow in marine environments, partly due to the accumulation of temperature-dependent regulatory incompatibilities within inversions.

Mitochondria respond to DNA damage and preserve their own genetic material in a manner distinct from that of the nucleus but that requires organized mito-nuclear communication. Failure to resolve mtDNA breaks leads to mitochondrial dysfunction and affects host cells and tissues. Here, we review the pathways that safeguard mitochondrial genomes and examine the insights gained from studies of cellular and tissue-wide responses to mtDNA damage and mito-nuclear genome incompatibility.

High‐throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with the computational demands of short‐read assemblies has posed significant laboratory and bioinformatics challenges for de novo genome assembly. Linked‐read or “synthetic long‐read” sequencing technologies, such as 10× Genomics, may provide a cost‐effective alternative solution to assemble higher quality de novo genomes from degraded tissue samples. Here, we compare assembly quality (e.g., genome contiguity and completeness, presence of orthogroups) between four new deer mouse (Peromyscus spp.) genomes assembled using linked‐read technology and four published genomes assembled from a single shotgun library. At a similar price‐point, these approaches produce vastly different assemblies, with linked‐read assemblies having overall higher contiguity and completeness, measured by larger N50 values and greater number of genes assembled, respectively. As a proof‐of‐concept, we used annotated genes from the four Peromyscus linked‐read assemblies and eight additional rodent taxa to generate a phylogeny, which reconstructed the expected relationships among species with 100% support. Although not without caveats, our results suggest that linked‐read sequencing approaches are a viable option to build de novo genomes from degraded tissues, which may prove particularly valuable for taxa that are extinct, rare or difficult to collect.

Background: Recent studies demonstrated that, in the past few years, the number of jellyfish species is increasing worldwide; this increase can be explained by environmental and climatic reasons. Contacts with jellyfish can cause acute and chronic effects, including allergic reactions. Although anaphylaxis caused by jellyfish is a rare event, repetitive stings during bathing as well as marine sports and job activities represent important risk factors that can increase the probability of sensitization. Recently, it was also pointed out the possibility of anaphylaxis caused by jellyfish ingestion. In these cases, the sensitization could also be related to previous stings. In cases in which there is no history of jellyfish contact or ingestion, it has been hypothesized that there is a sensitization to an unknown cross-reactive antigen. Objective: The purpose of this work was to collect and review published studies and cases of anaphylaxis associated with jellyfish. Methods: We performed a medical literature data base search, which included English language articles published until September 2019, by using the key words “jellyfish” associated with “anaphylaxis” or “anaphylactic shock.” Results: The results of our research showed that dangerous reactions can be caused both by contact and ingestion. Moreover, the latest changes in food habits, life style, and globalization could lead to a more frequent exposure to jellyfish both by contact and ingestion, and, consequently, to a higher probability of sensitization. Conclusion: Prospective studies and well-structured research are needed to better understand all the potential immunologic elements of jellyfish, to clarify its role in sensitization, and to avoid possible dangerous allergic reactions caused by cross-reactivity.

The role of recombination in genome evolution has long been studied in theory, but until recently empirical investigations had been limited to a small number of model species. Here, we compare the recombination landscape and genome collinearity between two populations of the Atlantic silverside (Menidia menidia), a small fish distributed across the steep latitudinal climate gradient of the North American Atlantic coast. We constructed separate linkage maps for locally adapted populations from New York and Georgia and their interpopulation laboratory cross. First, we used one of the linkage maps to improve the current silverside genome assembly by anchoring three large unplaced scaffolds to two chromosomes. Second, we estimated sex-specific recombination rates, finding 2.3-fold higher recombination rates in females than males-one of the most extreme examples of heterochiasmy in a fish. While recombination occurs relatively evenly across female chromosomes, it is restricted to only the terminal ends of male chromosomes. Furthermore, comparisons of female linkage maps revealed suppressed recombination along several massive chromosomal inversions spanning nearly 16% of the genome. These inversions segregate between locally adapted populations and coincide near perfectly with blocks of highly elevated genomic differentiation between wild populations. Finally, we discerned significantly higher recombination rates across chromosomes in the northern population compared to the southern. In addition to providing valuable resources for ongoing evolutionary and comparative genomic studies, our findings represent a striking example of structural variation that impacts recombination between adaptively divergent populations, providing empirical support for theorized genomic mechanisms facilitating adaptation despite gene flow.

Background: Tracheal intubation in patients with coronavirus disease-19 is a high-risk procedure that should be performed with personal protective equipment (PPE). The influence of PPE on operator’s performance during tracheal intubation remains unclear. Methods: We conducted a systematic review and meta-analysis of simulation studies to evaluate the influence of wearing PPE as compared to standard uniform regarding time-to-intubation (TTI) and success rate. Subgroup analyses were conducted according to device used and operator’s experience. Results: The TTI was prolonged when wearing PPE (eight studies): Standard Mean Difference (SMD)-0.54, 95% Confidence Interval [-0.75,-0.34], p < 0.0001. Subgroup analyses according to device used showed similar findings (direct laryngoscopy, SMD-0.63 [-0.88,-0.38], p < 0.0001; videolaryngoscopy, SMD-0.39 [-0.75,-0.02], p = 0.04). Considering the operator’s experience, non-anesthesiologists had prolonged TTI (SMD-0.75 [-0.98,-0.52], p < 0.0001) while the analysis on anesthesiologists did not show significant differences (SMD-0.25 [-0.51, 0.01], p = 0.06). The success rate of tracheal intubation was not influenced by PPE: Risk Ratio (RR) 1.02 [1.00, 1.04]; p = 0.12). Subgroup analyses according to device demonstrated similar results (direct laryngoscopy, RR 1.03 [0.99, 1.07], p = 0.15, videolaryngoscopy, RR 1.01 [0.98, 1.04], p = 0.52). Wearing PPE had a trend towards negative influence on success rate in non-anesthesiologists (RR 1.05 [1.00, 1.10], p = 0.05), but not in anesthesiologists (RR 1.00 [0.98, 1.03], p = 0.84). Trial-sequential analyses for TTI and success rate indicated robustness of both results. Conclusions: Under simulated conditions, wearing PPE delays the TTI as compared to dressing standard uniform, with no influence on the success rate. However, certainty of evidence is very low. Performing tracheal intubation with direct laryngoscopy seems influenced to a greater extent as compared to videolaryngoscopy. Similarly, wearing PPE affects more the non-anesthesiologists subgroup as compared to anesthesiologists.

Endotracheal intubation (ETI) in the pediatric setting is a complex skill and performing ETI during pediatric cardiopulmonary resuscitation is even more challenging. Simulation studies have investigated the performances of several devices for ETI. We undertook a systematic review and meta-analysis to evaluate the performances of devices for ETI during simulated pediatric on-going chest compressions. Devices were divided in four groups: direct laryngoscopy (DL) with Macintosh or Miller blade, or video-laryngoscopy with screen-on-device (VLS-SoD) or with distant monitor (VLS-DM). Primary outcomes were overall success rate (SR) and time-to-intubation (TTI). Results are expressed as Risk Ratio (RR) or Mean Difference (MD) with 95% confidence interval. We included 12 studies comparing at least two devices. The SR was greater for VLS as compared to DL-Miller (RR: 0.83 (0.78; 0.89), p < 0.00001) or DL-Macintosh (RR: 0.81 (0.77; 0.85), p < 0.00001). Subgroup analyses confirmed that both types of VLS were superior to DL-Miller (VLS-DM: p = 0.03; VLS-SoD: p < 0.00001) or DL-Macintosh (both VLSs: p < 0.00001). As compared with VLS, TTI was longer with both DL blades: Miller (MD: 8.26 seconds (5.30; 11.21), p < 0.00001) or Macintosh blade (MD: 7.63 seconds (4.14; 11.12), p < 0.00001). In the subgroup analyses, VLS-SoD was superior to DL-Miller or DL-Macintosh (both p < 0.00001), while VLS-DM was superior to DL-Macintosh (p < 0.00001), possibly not to DL-Miller (p = 0.06). Under simulated conditions of ongoing pediatric resuscitation, use of VLS guarantees higher overall SR and shorter TTI as compared to DL performed with Miller or Macintosh blade. Among VLSs, those with screen-on-device may have better performances that those with distant monitor.

Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages, recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localized change in the effective population size, potentially leading to an under or overestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.

The role of recombination in genome evolution has long been studied in theory, but until recently empirical investigations had been limited to a small number of model species. Here we compare the recombination landscape and genome collinearity between two populations of the Atlantic silverside (Menidia menidia), a small fish distributed across the steep latitudinal climate gradient of the North American Atlantic coast. Using ddRADseq, we constructed separate linkage maps for locally adapted populations from New York and Georgia and their inter-population lab cross. First, we used one of the linkage maps to improve the current silverside genome assembly by anchoring three large unplaced scaffolds to two chromosomes. Second, we estimated sex-specific recombination rates, finding 2.75-fold higher recombination rates in females than males—one of the most extreme examples of heterochiasmy in a fish. While recombination occurs relatively evenly across female chromosomes, it is restricted to only the terminal ends of male chromosomes. Furthermore, comparisons of female linkage maps revealed suppressed recombination along several massive chromosomal inversions spanning nearly 16% of the genome and segregating between locally adapted populations. Finally, we discerned significantly higher recombination rates across chromosomes in the northern population. In addition to providing valuable resources for ongoing evolutionary and comparative genomic studies, our findings represent a striking example of structural variation that impacts recombination between adaptively divergent populations, providing empirical support for theorized genomic mechanisms facilitating adaptation despite gene flow.

Marco Cavaleri,1 Stefano Tigano,1,2 Roberta Nicoletti,1,2 Valeria La Rosa,1,2 Alberto Terminella,3 Giacomo Cusumano,3 Filippo Sanfilippo,1 Marinella Astuto1,2 1Department of General Surgery and Medical-Surgical Specialties, Section of Anaesthesia and Intensive Care, University Hospital “G. Rodolico”, University of Catania, Catania, 95123, Italy; 2School of Anaesthesia and Intensive Care, University Hospital “G. Rodolico”, University of Catania, Catania, 95123, Italy; 3Thoracic Surgery Unit, Department of General Surgery and Medical-Surgical Specialties, University Hospital “G. Rodolico” - San Marco Hospital, Catania, 95121, ItalyCorrespondence: Marco CavaleriDepartment of General Surgery and Medical-Surgical Specialties, Section of Anaesthesia and Intensive Care, University Hospital “G. Rodolico”, University of Catania, Via Santa Sofia 78, Catania, 95123, ItalyTel +393339369927Email markuscava@gmail.comIntroduction: The erector spinae plane block (ESPB) is a recently implemented analgesic technique initially reported for thoracic analgesia and subsequently adopted for both intra- and postoperative pain management. Thoracic surgery is among the most painful surgical procedures, even when conducted with minimally invasive approach. Robotic-assisted thoracic surgery (RATS) challenges the traditional analgesic regimens as one of its aims is to decrease the patient’s length of stay (LOS) whilst achieving optimal postoperative pain management. Furthermore, there is lots of growing evidence on the impact of poorly controlled postoperative pain (PP) on the development of chronic post-surgical pain (CPSP). In these case series, we aim to describe our preliminary experience of postoperative pain management with continuous ESPB in the field of RATS.Case Series Presentation: In eight consecutive patients undergoing elective RATS procedure, we performed the ESPB after surgery with an initial bolus of local anesthetic followed by catheter insertion for continuous infusion. The infusion of local anesthetic lasted for the first two postoperative days. The effectiveness of the ESPB was evaluated through serial pain assessment with numeric rate scale (NRS) score, both at rest and during movement every 6 hours. Any analgesic rescue drug prescription was reported. We noted that the ESPB strongly reduced the prescription of opioids and of rescue analgesic. In our series, only one patient needed opioids during the first two postoperative days, and no rescue analgesic administration was noted in the remaining cases.Conclusion: We report a small but promising experience regarding postoperative pain management with continuous ESPB performed after RATS. We implemented the ESPB before surgery. Larger studies on postoperative pain management with continuous regional blocks in thoracic surgery are warranted.Keywords: pain management, regional block, thoracic surgery, postoperative care

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial selection-and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)—an established ecological model for studying the phenotypic effects of natural and artificial selection—and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32–1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

Hybridization can negatively impact one or both taxa involved and therefore pose conservation concerns. Climate change is expected to increase the rate of hybridization particularly in polar regions, and so investigating hybridization in Arctic and Antarctic species is important for conservation. Hybridization and genetic introgression have been observed between Pacific populations of thick-billed (Uria lomvia) and common murres (Uria aalge), species of seabirds with arctic and low arctic/temperate distributions, respectively. We employed double-digest restriction site-associated DNA sequencing (ddRADseq) to generate thousands of genome-wide markers to investigate hybridization and introgression in 133 thick-billed and 119 common murres sampled from 15 colonies throughout the North Atlantic. We used molecular assignments and principal components analysis to identify hybrids and quantify genetic introgression. Despite previous reports of hybridization between murre species in the Atlantic, we found no evidence for hybrid individuals in our dataset, and limited evidence for introgression. Our results suggest that hybridization between Atlantic murre species is rare, and does not currently pose a conservation concern for either species. Our study provides baseline data for monitoring hybridization between murres in the Atlantic to assess future impacts of climate change on these species.

The structure of the genome, including the architecture, number, and size of its chromosomes, shapes the distribution of genetic diversity and sequence divergence. Importantly, smaller chromosomes experience higher recombination rates than larger ones. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we adopted an integrative approach that combines empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different Mammalian clades - Peromyscus rodents, Mus mice, and great apes - from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades, but not the Mus clade, demonstrating that the dramatic chromosomal rearrangements among Mus species masked the ancestral genomic landscape of divergence in many comparisons. Moreover, our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different size is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge and eventually speciate, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations also revealed other factors that affect the relationship between chromosome size and divergence, including chromosomal rearrangements, demography, and divergence times, and deepen our understanding of the role of genome structure on the evolution of species divergence.

Background Inappropriate authors’ self-citation (A-SC) is a growing mal-practice possibly boosted by the raising importance given to author’s metrics. Similarly, also excessive journals’ self-citation (J-SC) practice may factitiously influence journal’s metrics (impact factor, IF). Evaluating the appropriateness of each self-citation remains challenging. Main body We evaluated the presence of policies discouraging A-SC in Critical Care Medicine (CCM) journals with IF. We also calculated the J-SC rate of these journals. In order to evaluate if J-SC rates are influenced by the focus of interest of CCM journals, we separated them in three sub-categories (“multidisciplinary”, “broad” or “topic-specific” CCM journals). We analyzed 35 CCM journals and only 5 (14.3%) discouraged excessive and inappropriate A-SC. The median IF was higher in CCM journals with A-SC policies [4.1 (3–12)] as compared to those without [2.5 (2–3.5); p = 0.02]. The J-SC rate was highly variable (0–35.4%), and not influenced by the presence of A-SC policies (p = 0.32). However, J-SC rate was different according to the focus of interest (p = 0.01): in particular, it was higher in “topic-specific” CCM journals [15.3 (8.8–23.3%)], followed by “broad” CCM [11.8 (4.8–17.9%)] and “multidisciplinary” journals [6.1 (3.6–9.1%)]. Conclusions A limited number of CCM journals have policies for limiting A-SC, and these have higher IF. The J-SC rate among CCM journals is highly variable and higher in “topic-specific” interest CCM journals. Excluding self-referencing practice from scientific metrics calculation could be valuable to tackle this scientific malpractice.

Schizophrenia pathophysiology is still not well understood. Genetic factors involving biochemical systems are key players and oxidative stress takes part to the development and worsening of SZ. Oxidative stress led to the permanent production of oxidation products such as advanced glycation end products (AGEs) and advanced oxidation protein products (AOPPs). These proteins interact with their receptor amplifying ROS production and pro-inflammatory cytokines sustaining a permanent loop. We tested plasma levels of AGEs and AOPPs in 30 SZ patients. Their levels were statistically higher than controls confirming their involvement in mental disorders. Antioxidant nutraceuticals and a healthy lifestyle could diminish oxidative stress and ameliorate SZ symptoms.

This paper deals with a monument that is, up to this date, unique in Sicily and in the Italian peninsula: the Mycenaean-type tholos tomb of the Gazzi necropolis in Messina. A recent excavation in the alluvial deposits revealed extensive traces of a funerary area with a tholos tomb and several enchytrismos tombs with skeletal remains, presumably dated back to the end of the Early or the initial stage of the Middle(?) Bronze Age. The present multi-disciplinary investigation has been developed to analyse new data related to sediments, building stones and skeletal remains of this funerary area. The stratigraphic succession hosting the necropolis was formed by overbank sediments deposited on the alluvial floodplain of the Gazzi palaeostream and developed during a regressive trend. The tholos building stones were opportunely selected and distributed in the different sectors of the tomb. The crystalline building stones are unworked stones derived from the alluvial pebbles of the palaeostream, whereas the worked stones are derived from local quarries of limestones located in the surrounding hills. The osteological remains are ascribable exclusively to Homo. The minimum number of individuals inside the tholos was calculated to consist of one adult, whereas one adult and one infant were found in the enchytrismos burials. The Gazzi necropolis discovery demonstrates the important role played by the Messina settlements during the Bronze Age, when relationships between the Aegean and Western world became closer.

Single molecule analysis of replicating DNA (SMARD) is a powerful methodology that allows in vivo analysis of replicating DNA; identification of origins of replication, assessment of fork directionality, and measurement of replication fork speed. SMARD, which has been extensively used to study replication of nuclear DNA, involves incorporation of thymidine analogs to nascent DNA chains and their subsequent visualization through immune detection. Here, we adapt and fine-tune the SMARD technique to the specifics of human and mouse mitochondrial DNA. The mito-SMARD protocol allows researchers to gain in vivo insight into mitochondrial DNA (mtDNA) replication at the single molecule level and with high resolution.

Single molecule analysis of replicating DNA (SMARD) is a powerful methodology that allows in vivo analysis of replicating DNA; identification of origins of replication, assessment of fork directionality, and measurement of replication fork speed. SMARD, which has been extensively used to study replication of nuclear DNA, involves incorporation of thymidine analogs to nascent DNA chains and their subsequent visualization through immune detection. Here, we adapt and fine-tune the SMARD technique to the specifics of human and mouse mitochondrial DNA. The mito-SMARD protocol allows researchers to gain in vivo insight into mitochondrial DNA (mtDNA) replication at the single molecule level and with high resolution.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363genomes from 92.4% of bird families-including 267newly sequenced genomes produced for phaseII of the Bird 10,000Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10X Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia) - an established ecological model for studying the phenotypic effects of natural and artificial selection - and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is the highest reported for a fish, or any vertebrate, to date (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ~23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

The importance of structural variation in adaptation and speciation is becoming increasingly evident in the literature. Among SVs, copy number variants (CNVs) are known to affect phenotypes through changes in gene expression and can potentially reduce recombination between alleles with different copy numbers. However, little is known about their abundance, distribution and frequency in natural populations. In a "From the Cover" article in this issue of Molecular Ecology, Dorant et al. (2020) present a new cost-effective approach to genotype copy number variants (CNVs) from large reduced-representation sequencing (RRS) data sets in nonmodel organisms, and thus to analyse sequence and structural variation jointly. They show that in American lobsters (Homarus americanus), CNVs exhibit strong population structure and several significant associations with annual variance in sea surface temperature, while SNPs fail to uncover any population structure or genotype-environment associations. Their results clearly illustrate that structural variants like CNVs can potentially store important information on differentiation and adaptive differences that cannot be retrieved from the analysis of sequence variation alone. To better understand the factors affecting the evolution of CNVs and their role in adaptation and speciation, we need to compare and synthesize data from a wide variety of species with different demographic histories and genome structure. The approach developed by Dorant et al. (2020) now allows to gain crucial knowledge on CNVs in a cost-effective way, even in species with limited genomic resources.

Il saggio esamina alcuni tratti problematici insiti nell’esercizio della funzione di ordine pubblico, al fine di evidenziarne la complessità e talora la contraddittorietà, anche con principi acclarati e potenzialmente ineludibili come quello di trasparenza, al punto da mettere in discussione la permanenza stessa del principio di legalità. Si tratta di riflessioni che spaziano liberamente su numerosi versanti, la cui finalità non può che essere esemplificativa e cionondimeno – almeno si stima – altrettanto significativa. Nel contempo, viene evidenziata l’esistenza di un livello macro e di un livello micro nella esplicazione della funzione e pur essendo assai rilevante e notoriamente preponderante il primo rispetto al secondo nell’ambito delle attività di contrasto ai fenomeni di illegalità in genere – in grado di incidere sull’ordine pubblico in misura determinante – il secondo non va del tutto abbandonato in quanto suscettibile di determinare la percezione o meno di una illegalità diffusa, infine ricadente sulle libertà dei singoli, la cui rilevanza non può essere misconosciuta. In definitiva, da un lato si stima di aprire una riflessione sulle “latitudini” della funzione in sé, dall’altro, si prende posizione relativamente a recenti interventi in materia di ordine e sicurezza pubblico, talora additati sul piano della loro compatibilità costituzionale, che, a ben guardare, sono anche frutto di esigenze presenti nelle collettività sociali e nella vita dei singoli cittadini. The essay examines some problematic features inherent the exercise of the function of public order, to highlight the complexity and sometimes the contradiction, even with established and potentially unavoidable principles, such as transparency, to the point of questioning the very permanence of the legality principle. Those reflections range freely on numerous sides, whose purpose can only be an example and nevertheless - at least it is estimated - equally significant. At the same time, the existence of a macro level and a micro level in the explanation of the function is highlighted and while the former is very relevant and notoriously predominant compared to the latter in the context of activities to combat illegal phenomena in general - capable of affect public order to a decisive extent - the latter must not be completely abandoned as it can determine the perception or not of a widespread illegality, capable of affecting the freedoms of individuals, whose relevance cannot be misunderstood. Ultimately, on the one hand, it is estimated to open a reflection on the "latitudes" of the function itself, on the other, it takes a position on recent interventions in the field of public order and security, sometimes pointed out in terms of their constitutional compatibility, which, on closer inspection, are also the result of needs present in social collectives and in the lives of citizens., P.A. Persona e Amministrazione, N. 1 (2020)